Quote Originally Posted by KrayZ33
Hmm, since a geass affects the brainwaves of the one its used against, (at least Lelouch's does i think, it was mentioned in season 1) its probably the same thing with his own brain.

It could be the case that his brain can't shut of the geass, because it got used to its activation.
Well, if his memories are rewritten, it could have an effect on his brainwaves and his brain is like: "hey, for what is this switch here?... hmm i can't remember it so its better to turn it off"

(crappy explanation because of ultra-low english skills, it has to do with neurons etc. but thats too hard for me to explain)
Basically, if one of the processes or variable is rewriten, you break the loop and the Geass can't work. Once le processes are back to normal, Geass is reactivated.
For neurons, that could mean that a part of the route needed to activate the Geass is not accessible due to the rewrite that basically is a change of neural routes. No route going to the activation means no Geass.

Basically simple, just a clever use the Emperor would make, which is basically very consistent with him having his Geass for a long time and being a very strong mastermind.